More posts like this
-
Convert alleles from Illumina 1/2 format to ACGT format?
written by dam4l 20Hi everyone, I have a binary PLINK fileset in which alleles are coded 1/2 and failed calls are denoted by 0. The 1/2 format is …
-
SNP filtering
written by rheab1230 15Hello everyone, I am trying to filter .vcf files to contain only single point SNP and remove indel. I have remove indel from the .vcf …
-
Ambiguous SNPs
written by nhaus 44I am currently reading up about Genotype Arrays and the different nomenclatures that are used to report genotypes. In that context, it is important if …
-
Types of base substitutions
written by Gene_MMP8 25I was reading this Wikipedia article on Mutational Signatures and I came across this section titled **Types of mutations: base substitutions**. I don't understand why …
-
visualizing mutational data using Maftools for reference genome hg19
written by nazaninhoseinkhan 53Dear all, I am trying to do somatic variation analysis using TCGABiolinks package in R 3.6. I want to use hg19 version of human genome. …
-
GATK data-preprocessing omit Indelrealignment step
written by 9521ljh 5I also read this article. https://software.broadinstitute.org/gatk/blog?id=7847 However, i'm not clear why Indelrealignmnet Step is omitted. In this article, i understand like that When using Mutect2 …
-
Group mutations in SNP data
written by nanana 12I have some somatic SNP data for multiple tumour normal comparisons that I'm exploring in plots such as [this][1] This plot shows the contribution each …
-
How to only show SNPs in vcf files
written by Joe 3I have some vcf file generated by using GATK Unified Genotyper (--output_mode **EMIT_ALL_SITES**), it looks like chr15 21138918 . C . 46.23 . . GT:DP …
-
understanding of dbSNP info on MAF, Alleles and HGVS Names
written by tonja.r 60I have some problems with understanding of the concepts of SNP and related MAF, Alleles and NGVS Names. I was looking at rs2476601. From "Allele" …
-
In R, how do I apply regexes to specific parts of a string that contains a pattern?
written by soosus 1I have a dataframe (**trip**) that contains a column (**SNP**). It looks like this (but longer, and it has 192 levels): SNP C[T->C]T C[G->C]A G[A->C]A …
copy/pasted:
Because the pyrimidine base of the Watson-Crick base-pair has become a community standard.https://github.com/PoisonAlien/maftools/issues/510
in the code (https://rdrr.io/bioc/maftools/src/R/TrinucleotideMatrix.R):